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- PDB-1hfk: Asparaginase from Erwinia chrysanthemi, hexagonal form with weak ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hfk | ||||||
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Title | Asparaginase from Erwinia chrysanthemi, hexagonal form with weak sulfate | ||||||
![]() | L-ASPARAGINE AMIDOHYDROLASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lubkowski, J. / Palm, G.J. / Kozak, M. / Jaskolski, M. / Wlodawer, A. | ||||||
![]() | ![]() Title: Structures of Two Highly Homologous Bacterial L-Asparaginases: A Case of Enantiomorphic Space Groups Authors: Jaskolski, M. / Kozak, M. / Lubkowski, J. / Palm, G.J. / Wlodawer, A. #1: ![]() Title: Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy Authors: Swain, A.L. / Jaskolski, M. / Housset, D. / Rao, J.K.M. / Wlodawer, A. #2: Journal: FEBS Lett. / Year: 1993 Title: A Left-Handed Crossover Involved in Amidohydrolase Catalysis, Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate Authors: Miller, M. / Rao, J.K.M. / Wlodawer, A. / Gribskov, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 106.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 330.8 KB | Display | ![]() |
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Full document | ![]() | 341.1 KB | Display | |
Data in CIF | ![]() | 793 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hfjSC ![]() 1ho3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.989565, -0.016041, -0.143189), Vector: Details | BIOLOGICAL_UNIT: HOMOTETRAMERIN THE TETRAMER TWO ACTIVE SITES ARE FORMED BY EACH INTIMATE DIMER AC AND ITS CRYSTALLOGRAPHIC SYMMETRY MATE | |
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Components
#1: Protein | Mass: 35123.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI. Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | RESIDUES 1 TO 21 IN THE DATABASE ENTRY CONSTITUTE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400. CRYSTALS CROSSLINKED WITH 0.05% GLUTARALDEHYDE. SOAKED IN 40% PEG 6000, ...Details: HANGING DROP. PROTEIN SOLUTION: 35 MG/ML PROTEIN, 0.1 M CHES PH 8.5. WELL SOLUTION: 47% AMMONIUM SULFATE, 2% PEG 400. CRYSTALS CROSSLINKED WITH 0.05% GLUTARALDEHYDE. SOAKED IN 40% PEG 6000, 100 MM NAOAC, 100 MM 4-HYDROXY- LYSINE, PH 5.5. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.8 / Method: vapor diffusion / Details: Kozak, M., (2000) Acta Biochim. Pol., 47, 807. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→20 Å / Num. obs: 29191 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.118 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.17→2.25 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.373 / % possible all: 71 |
Reflection | *PLUS Num. measured all: 128226 / Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS % possible obs: 71 % / Rmerge(I) obs: 0.373 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HFJ Resolution: 2.17→10 Å / Rfactor Rfree error: 0.0076 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: MLF (MAXIMUM LIKELYHOOD ON F'S)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.03 Å2
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Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.2 Å / Total num. of bins used: 22 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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